gwy_converter

Uses Gwyddion to convert SPM (scanning probe microscopy) files into well-supported data-interchange format.

Uses Nix to produce artefacts in a completely reproducible fashion.

Installation and usage

$ git clone https://github.com/antoinerg/gwy_converter
$ cd gwy_converter

Convert local files

$ # the path argument has to be an absolute path!
$ nix-build convert.nix --argstr path "/absolute_path_to_afm_file.sxm"
$ tree result
result
├── channel
│   ├── 00
│   │   ├── channel.json
│   │   └── image.png
│   ├── 01
│   │   ├── channel.json
│   │   └── image.png
... snip ... snip ...
│   ├── 20
│   │   ├── channel.json
│   │   └── image.png
│   └── 21
│       ├── channel.json
│       └── image.png
├── data.gwy
└── image.json

23 directories, 46 files

Convert files served via HTTP

$ nix-build convert.nix \
  --argstr url "http://localhost:8080/ipfs/QmaEApiJT26NSF4MWhMBuyxno5zP2ifNBqNkoQSLX8Vb7r" \
  --argstr sha256 "a263a06015c02e292b3a6a6817c0c68dba047eec8a4dc463e6d240cc827c9369"

Development

About running Gwyddion on NixOS

In order to compile Gwyddion with pygwy module under NixOS, we need to patch the configure script as shown here.

Running

PYTHONPATH=result/lib/python2.7/site-packages/:PYTHONPATH xvfb-run ./test.py /mnt/data/nanonis/2015-03-inas_capped/raw/28-03-2015.inas_capped.001.sxm